GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
S-AdoMet_synt_M - S-adenosylmethionine synthetase central domain
Pfam: PF02772 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Length: 120
Sequences: 1921
Seq/Len: 16.01
HH_delta: -0.007 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
34_A55_S1.166133.725
60_E69_R1.136043.629
21_E28_V1.094943.497
85_L89_R1.043313.333
36_R39_E0.895512.860
71_D111_K0.824692.634
48_W91_D0.797872.549
94_E98_K0.791962.530
35_R39_E0.733072.342
69_R107_D0.714432.282
75_V92_I0.703162.246
25_L29_L0.685212.189
84_S87_E0.665812.127
27_I31_H0.662262.115
39_E43_N0.656382.097
93_K98_K0.633942.025
34_A53_G0.626682.002
73_I101_I0.581961.859
72_T113_L0.578021.846
90_E94_E0.576451.841
87_E91_D0.572451.829
32_R35_R0.561221.793
76_S116_P0.559631.788
36_R99_P0.547151.748
38_A42_K0.536461.714
89_R93_K0.50641.618
106_L112_I0.503931.610
45_E95_K0.486511.554
102_P105_L0.479461.532
107_D110_T0.453511.449
86_E89_R0.442681.414
91_D95_K0.438411.400
33_L75_V0.435861.392
92_I114_I0.431091.377
86_E90_E0.42171.347
97_I112_I0.416181.329
72_T111_K0.406531.299
21_E32_R0.403061.287
36_R40_V0.391431.250
37_L53_G0.391271.250
60_E107_D0.391181.250
28_V35_R0.390431.247
40_V53_G0.390251.247
50_R80_D0.384071.227
50_R81_E0.383641.225
95_K99_P0.367731.175
70_I101_I0.346661.107
28_V32_R0.344881.102
59_V70_I0.343911.099
40_V96_V0.339951.086
46_L91_D0.338091.080
58_T71_D0.327681.047
74_V114_I0.326481.043
83_I88_I0.320351.023
40_V46_L0.311130.994
37_L96_V0.308980.987
25_L59_V0.307840.983
37_L77_T0.305120.975
69_R109_D0.305110.975
101_I106_L0.30340.969
16_C22_L0.297060.949
12_F77_T0.294030.939
48_W88_I0.291780.932
34_A37_L0.2910.930
26_P67_P0.282950.904
49_L77_T0.276290.883
98_K103_E0.273490.874
48_W83_I0.271320.867
73_I106_L0.270920.865
17_D66_K0.264370.844
81_E119_R0.264180.844
22_L26_P0.262150.837
6_G9_G0.260530.832
106_L110_T0.259250.828
77_T92_I0.256440.819
60_E63_E0.252150.805
70_I112_I0.250440.800
11_M23_M0.249980.798
92_I96_V0.245870.785
60_E71_D0.244860.782
83_I87_E0.241320.771
40_V49_L0.240150.767
37_L92_I0.23780.760
25_L105_L0.23680.756
36_R96_V0.234890.750
23_M27_I0.232370.742
4_G9_G0.23210.741
33_L57_V0.229420.733
83_I91_D0.229360.733
78_Q120_F0.22910.732
10_I25_L0.226380.723
37_L75_V0.2260.722
85_L88_I0.224680.718
37_L40_V0.223990.715
74_V113_L0.219480.701
50_R88_I0.219380.701
93_K114_I0.217810.696
58_T72_T0.217610.695
47_P80_D0.215520.688
56_Q76_S0.215470.688
87_E90_E0.212150.678
26_P59_V0.210190.671
48_W87_E0.209480.669
9_G76_S0.208710.667
36_R100_V0.207780.664
65_G68_V0.206770.660
3_I59_V0.205130.655
93_K97_I0.204920.655
30_A55_S0.20460.654
40_V45_E0.203630.650
88_I91_D0.200570.641
46_L92_I0.199440.637
5_A9_G0.196630.628
23_M28_V0.196510.628
96_V99_P0.1960.626
38_A41_R0.193170.617
113_L119_R0.191390.611
88_I115_N0.190860.610
29_L57_V0.190650.609
93_K112_I0.190020.607
86_E109_D0.190010.607
85_L117_T0.189820.606
102_P112_I0.189550.605
66_K104_Y0.187870.600
79_H120_F0.187020.597
34_A38_A0.184840.590
36_R45_E0.184430.589
46_L88_I0.18430.589
46_L49_L0.183190.585
70_I97_I0.182020.581
53_G115_N0.18180.581
17_D20_P0.181780.581
30_A34_A0.181150.579
55_S75_V0.178830.571
87_E95_K0.178810.571
38_A53_G0.177580.567
10_I27_I0.175930.562
37_L99_P0.175550.561
37_L49_L0.175380.560
59_V105_L0.175320.560
26_P68_V0.17520.560
48_W80_D0.175020.559
57_V60_E0.1750.559
34_A96_V0.174530.557
53_G77_T0.17430.557
75_V101_I0.174140.556
49_L75_V0.173720.555
115_N118_G0.172690.552
39_E45_E0.172630.551
4_G7_D0.171020.546
68_V107_D0.169670.542
101_I105_L0.169170.540
63_E68_V0.16790.536
53_G75_V0.167440.535
6_G18_E0.166830.533
27_I34_A0.166070.530
16_C28_V0.165210.528
81_E90_E0.16490.527
6_G79_H0.164360.525
9_G56_Q0.16320.521
99_P103_E0.162650.520
49_L63_E0.162480.519
5_A54_K0.161450.516
8_Q11_M0.159350.509
31_H38_A0.158350.506
61_Y67_P0.158160.505
95_K98_K0.156970.501
35_R38_A0.156870.501
43_N108_E0.156540.500
31_H35_R0.155020.495
33_L95_K0.15270.488
10_I63_E0.15220.486
88_I96_V0.151740.485
72_T75_V0.151230.483
47_P82_D0.150860.482
40_V99_P0.150570.481
28_V80_D0.15020.480
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
3imlA0.9917100-0.007
3s82A0.9917100-0.002
3so4A11000.001
1p7lA0.99171000.004
2p02A11000.014
1u04A0.408368.60.932
3pc3A0.683363.10.934
1yvuA0.391744.70.941
1mp9A0.541735.70.944
2w42A0.4917340.944

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